Problem in retrieving the transmission from a sile

[Mero62]

Hi Nick, Hope you're doing alright! I have an occuring issue that never happened before. I'm calculating the transmission of a pristine Nanoribbon. So far so good, however having used Tbtrans to generate some siesta.TBT.nc file, I can retrieve the energy but not the transmission which never happened before. Here is the line of code that shows the issue :

tbt_pristine = sisl.get_sile('siesta.TBT.nc')
print(tbt_pristine.transmission())

I get the following error message :

TypeError                                 Traceback (most recent call last)
<ipython-input-17-de5116be1d52> in <module>
      1 os.chdir('/home/kucukbam/Desktop/PHD/Python/Programs/Machine_learning/Datas_long_thin_zGNR_5imp')
      2 tbt_pristine = sisl.get_sile('siesta.TBT.nc')
----> 3 print(tbt_pristine.transmission())

~/miniconda3/lib/python3.7/site-packages/sisl/io/tbtrans/tbt.py in transmission(self, elec_from, elec_to, kavg)
    218             raise ValueError(self.__class__.__name__ + ".transmission elec_from and elec_to must not be the same.")
    219 
--> 220         return self._value_avg(elec_to + '.T', elec_from, kavg=kavg)
    221 
    222     def reflection(self, elec=0, kavg=True, from_single=False):

TypeError: unsupported operand type(s) for +: 'int' and 'str'

[zerothi]

Hmm, could you give me the output of

ncdump -h siesta.TBT.nc

? Thanks!

[Mero62]

Of course. Here is the output :

netcdf siesta.TBT {
dimensions:
    no_u = 240 ;
    na_u = 240 ;
    nkpt = 1 ;
    xyz = 3 ;
    one = 1 ;
    na_d = 200 ;
    no_d = 200 ;
    ne = 50 ;
    n_s = 3 ;
variables:
    int lasto(na_u) ;
        lasto:info = "Last orbitals of the equivalent atom" ;
    double cell(xyz, xyz) ;
        cell:unit = "Bohr" ;
        cell:info = "Unit cell" ;
    double xa(na_u, xyz) ;
        xa:unit = "Bohr" ;
        xa:info = "Atomic coordinates" ;
    int isc_off(n_s, xyz) ;
        isc_off:info = "Supercell offsets" ;
    int nsc(xyz) ;
        nsc:info = "Number of supercells in each direction" ;
    int pivot(no_d) ;
        pivot:info = "Device region orbital pivot table" ;
    int a_dev(na_d) ;
        a_dev:info = "Index of device atoms" ;
    double kpt(nkpt, xyz) ;
        kpt:unit = "b" ;
        kpt:info = "k point" ;
    double wkpt(nkpt) ;
        wkpt:info = "k point weights" ;
    double E(ne) ;
        E:unit = "Ry" ;
        E:info = "Energy" ;

// global attributes:
        :source = "TBtrans" ;
        :Gamma = "false" ;
        :date = "2020-07-09" ;

group: Bottom {
  variables:
    double mu(one) ;
        mu:unit = "Ry" ;
        mu:info = "Chemical potential" ;
    double kT(one) ;
        kT:unit = "Ry" ;
        kT:info = "Electronic temperature" ;
    float Top.T(nkpt, ne) ;
        Top.T:info = "Transmission" ;
  } // group Bottom
}

Oh yeah by the way, I don't know how much it has do with the current issue but it seems by the previous error that something went wrong with the electrode configuration so I double checked it without seeing an issue in my fdf file. However when one tries to retrieve information about electrodes through the .elecs method (so when you have something like print (tbt_pristine.elecs), I just get the first electrode in the TBT.elecs block... It might be normal but I thought it was worth pointing it out here.

[zerothi]

Ahh, now I get it. This is because the latest tbtrans will always write out more stuff in the NetCDF files. So I would suggest you to download this and recompile tbtrans :)

[Mero62]

Dear Nick, Sorry for the delay, I recompiled TBtrans with this version and thank you, it worked as usual ;)

[zerothi]

Great, I'll consider this solved! Thanks for the question!